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cran · Nov 1, 2024 · aecf52e · aecf52e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,24 +1,25 @@
 Package: landscapeR
+Type: Package
 Title: Categorical Landscape Simulation Facility
-Version: 1.2
-Date: 2017-07-05
-Authors@R: c(person(given = "Dario", family = "Masante", role = c("aut", "cre"), email = "[email protected]"))
+Version: 1.3
+Date: 2024-10-31
+Authors@R: c(person(given = "Dario", family = "Masante", role = c("aut", "cre"), email = "[email protected]"), person(given="Lora", family="Murphy", role="ctb", email="[email protected]"))
+Maintainer: Dario Masante <[email protected]>
 Copyright: Natural Environment Research Council (NERC) and Centre for
         Ecology and Hydrology (CEH)
 URL: https://github.com/dariomasante/landscapeR
 BugReports: https://github.com/dariomasante/landscapeR/issues
-Imports: raster, Rcpp
-Suggests: knitr, rmarkdown
 Description: Simulates categorical maps on actual geographical realms, starting from either empty landscapes or landscapes provided by the user (e.g. land use maps). Allows to tweak or create landscapes while retaining a high degree of control on its features, without the hassle of specifying each location attribute. In this it differs from other tools which generate null or neutral landscapes in a theoretical space. The basic algorithm currently implemented uses a simple agent style/cellular automata growth model, with no rules (apart from areas of exclusion) and von Neumann neighbourhood (four cells, aka Rook case). Outputs are raster dataset exportable to any common GIS format.
-License: GPL (>= 3)
-LazyLoad: yes
-LazyData: TRUE
-NeedsCompilation: yes
-RoxygenNote: 6.0.1
+License: GPL (>= 2)
+Imports: terra, Rcpp (>= 1.0.3)
+Suggests: markdown, knitr
 VignetteBuilder: knitr
 LinkingTo: Rcpp
-Packaged: 2017-07-05 12:46:53 UTC; masanda
-Author: Dario Masante [aut, cre]
-Maintainer: Dario Masante <[email protected]>
+RoxygenNote: 7.3.2
+Encoding: UTF-8
+NeedsCompilation: yes
+Packaged: 2024-11-01 20:18:02 UTC; masante
+Author: Dario Masante [aut, cre],
+  Lora Murphy [ctb]
 Repository: CRAN
-Date/Publication: 2017-07-05 14:54:40 UTC
+Date/Publication: 2024-11-01 21:10:02 UTC
diff --git a/MD5 b/MD5
@@ -1,26 +1,38 @@
-635cbadccce3f453f67e0a3700dd9fb2 *DESCRIPTION
+ec18e2ccb5dd767ede9dd4667618c269 *DESCRIPTION
 8cb35e234ffdef13f971f80f618992d6 *NAMESPACE
-c6d36ae0e1a07ab41f1e636a73666f21 *NEWS.md
-66325721520b6166fc43b30120d92efe *R/RcppExports.R
-e5bc5591c800db13c86bfc9d3ce35a61 *R/expandClass.R
-cf831291457e08215afcca621c9464dd *R/landscapeR-package.R
-bdf9b4d20560afbd60d521a1fbf2e732 *R/makeClass.R
-1a345dd95f03a3f5a1d521de23f4fc92 *R/makeLine.R
-5551b59d16704db38c520670ace84a86 *R/makePatch.R
-f88406fe7e71b669fa84ad396486a799 *R/rmSingle.R
-332b9e5c43055838eef2af68eb49f3bf *R/zzz.R
-892f937b1044f7090ff6980db2c7a0af *build/vignette.rds
+4057d20c5d9ee89b2d4ea419eaba577e *NEWS.md
+a4ab04b34a6d2113834a96da10f06bb1 *R/RcppExports.R
+168ca0ccf582456039467371f1e83157 *R/expandClass.R
+b9d53aa85ad2c547d7c52f4a9f34b059 *R/landscapeR-package.R
+af244cdb4ac0364338618cf8c136f9e5 *R/makeClass.R
+6ffbe05f5adca845f4a31d47e5ae01ab *R/makeLine.R
+2e938d300cc5794a3da6c914c703dd41 *R/makePatch.R
+7ba55e788d85d98272daaa8293a6d9b9 *R/rmSingle.R
+87f902189223e5c7d422ad9c0939bfb1 *R/zzz.R
+d8f455396216d93c4566d2e7d27c79c0 *build/vignette.rds
+62583f9b09873cae8b1462ab7a194b29 *inst/CITATION
 6fbe40d2a4c543685ea49b7d68d82b2c *inst/COPYRIGHTS
-7b735af5155c2c74c559cde104f62bac *inst/doc/landscapeR.R
-96aa2511ef0b7ba5105ce2f91c068ecf *inst/doc/landscapeR.Rmd
-4030c8bb7fe2d0cd92e6c34da759fca8 *inst/doc/landscapeR.html
-898c0bf34293df5b324bb37c4a6bd7d0 *man/expandClass.Rd
-2d65e8077c0e3ec6352d517541dc35c0 *man/landscapeR-package.Rd
-1dd5e286a3562d5dec8ebb27b0d090c9 *man/makeClass.Rd
-cc68acb717a59cb4692a2354f757df59 *man/makeLine.Rd
-ad9f5a48e5e8bf83366a82e68ea2997b *man/makePatch.Rd
-32fc6e2675d2583c2551aa0f11fa07db *man/rmSingle.Rd
-a947e62ede9bc4c0b93d4cc252d078fe *src/RcppExports.cpp
+252f0946024f3bbf733966c6d6491bc3 *inst/doc/landscapeR.R
+c83a1bf9c22389834a2386e938d7ca95 *inst/doc/landscapeR.Rmd
+d87cbd9624b2bb5e3b896320761a9e41 *inst/doc/landscapeR.html
+cf0295d2d592fbc5ed8a1af87bd955ea *man/expandClass.Rd
+d6702d535b78103d3d2fc871b5f141c5 *man/landscapeR-package.Rd
+82cf92f26f6a6c7647c1fab4cf6e7e69 *man/makeClass.Rd
+4f25d11d502ba8675fabf33a4130ea40 *man/makeLine.Rd
+92c7f17b4a82f8599b8d284c470c5ee0 *man/makePatch.Rd
+b517983d400497707a97cf95e66a5105 *man/rmSingle.Rd
+e54b43411f0dfd289205a84ef2f54ad3 *src/RcppExports.cpp
 a75ee32e13bfc69ed50076851d2c5806 *src/hidden.cpp
-0492eaed7b43f1b319e7d4ade16a607f *src/init.c
-96aa2511ef0b7ba5105ce2f91c068ecf *vignettes/landscapeR.Rmd
+c83a1bf9c22389834a2386e938d7ca95 *vignettes/landscapeR.Rmd
+313c6f0599ccc474c1b06e1276c59212 *vignettes/unnamed-chunk-10-1.png
+0a5c0fbb64c8ea2043ddf75aa03520ec *vignettes/unnamed-chunk-11-1.png
+19c27aee4ba9df1340a5b8d513336db2 *vignettes/unnamed-chunk-12-1.png
+85d3ac8ed33aeec12c518b2352e6ad8b *vignettes/unnamed-chunk-13-1.png
+606dd60c9f9f40f704505284fdf53cad *vignettes/unnamed-chunk-14-1.png
+62406792a0fa29e5f8c82c2e55bffab9 *vignettes/unnamed-chunk-15-1.png
+22830f630e0d80715395620aa8460fed *vignettes/unnamed-chunk-3-1.png
+af089806b6d9cc49d826296ffd1b4d61 *vignettes/unnamed-chunk-4-1.png
+b52966a06f38e4b42aa758f8f7b872e4 *vignettes/unnamed-chunk-5-1.png
+3f61be83400ce8b45e74c6b426d95da9 *vignettes/unnamed-chunk-6-1.png
+7d7be70420416c176496a5d3ecd22f6a *vignettes/unnamed-chunk-8-1.png
+e5613818fa82a525d27fcbc7a73acc2b *vignettes/unnamed-chunk-9-1.png
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,17 @@
+landscapeR v1.3 (Release date: 2024-10-31)
+-----------------------------------------------
+CHANGES:
+* use package terra instead of raster
+* Fixing data types for Rcpp
+* Added options for vector value to makeClass
+
+landscapeR v1.2.1 (Release date: 2020-02-05)
+-----------------------------------------------
+CHANGES:
+
+* Added Ecological Applications paper citation
+
+
 landscapeR v1.2 (Release date: 2017-07-05)
 -----------------------------------------------
 CHANGES:

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -2,14 +2,14 @@
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 .contigCells <- function(pt, bgr, mtx) {
-    .Call("landscapeR_contigCells_cpp", PACKAGE = "landscapeR", pt, bgr, mtx)
+    .Call("_landscapeR_contigCells_cpp", PACKAGE = "landscapeR", pt, bgr, mtx)
 }
 
 .assignValues <- function(val, ad, mtx) {
-    .Call("landscapeR_assignValues_cpp", PACKAGE = "landscapeR", val, ad, mtx)
+    .Call("_landscapeR_assignValues_cpp", PACKAGE = "landscapeR", val, ad, mtx)
 }
 
 .indexTranspose <- function(id, dim1, dim2) {
-    .Call("landscapeR_indexTranspose_cpp", PACKAGE = "landscapeR", id, dim1, dim2)
+    .Call("_landscapeR_indexTranspose_cpp", PACKAGE = "landscapeR", id, dim1, dim2)
 }
 
diff --git a/R/expandClass.R b/R/expandClass.R
@@ -5,12 +5,13 @@
 #' @param class The raster value of class (or patch) to expand.
 #' @param size integer. Size of expansion, as number of raster cells.
 #' @param bgr integer. The background available where expansion is allowed (i.e. shrinking classes).
-#" @return A RasterLayer object. If \code{rast=FALSE} returns a list of vectors, each containing the \code{context} cells assigned to each patch.
+#" @return A SpatRaster object. If \code{rast=FALSE} returns a list of vectors, each containing the \code{context} cells assigned to each patch.
 #' @examples
-#" library(raster)
+#" library(terra)
 #'
 #' m = matrix(0, 33, 33)
-#' r = raster(m, xmn=0, xmx=10, ymn=0, ymx=10)
+#' r = rast(m)
+#' ext(r) = c(0, 10, 0, 10)
 #' r = makeClass(r, 5, 10)
 #' plot(r)
 #'
@@ -19,7 +20,8 @@
 #'
 #' ## This function can be used to mimic shapes, by providing a skeleton:
 #' m[,17] = 1
-#' r = raster(m, xmn=0, xmx=10, ymn=0, ymx=10)
+#' r = rast(m)
+#' ext(r) = c(0, 10, 0, 10)
 #' plot(r)
 #'
 #' rr = expandClass(r, 1, 100)
@@ -29,10 +31,14 @@ expandClass <- function(context, class, size, bgr=0, pts = NULL) {
   if(length(class) > 1){ stop('A single value only is admitted for "class" argument.') }
   if(class %in% bgr){ warning('Value to attribute to patches same as background cells value (arg. "class" equals "bgr").') }
   if(any(is.na(size) | size <=0)){ stop('Invalid "size" argument provided.') }
-  bd <- raster::boundaries(context, type='outer', classes=TRUE, directions=8)
-  bd <- t(raster::as.matrix(bd))
+  bd <- terra::boundaries(context, inner=FALSE, classes=TRUE, directions=8)
+  #----- LEM: the as.numeric is required for type matching in Rcpp -----------#
+  bd <- terra::as.matrix(bd, wide=T)
+  bd <- t(matrix(as.numeric(bd), ncol=ncol(bd), nrow=nrow(bd)))
   if(!is.matrix(context)) {
-    mtx <- t(raster::as.matrix(context))
+    #----- LEM: the as.numeric is required for type matching in Rcpp ---------#
+    mtx <- terra::as.matrix(context, wide=T)
+    mtx <- t(matrix(as.numeric(mtx), ncol=ncol(mtx), nrow=nrow(mtx)))
   } else {
     mtx <- context
   }
@@ -90,6 +96,6 @@ expandClass <- function(context, class, size, bgr=0, pts = NULL) {
 #    mtx[p_bgr[id]] <- vals[id]
     mtx[.subset(p_bgr, id)] <- .subset(vals, id)
   }
-  context[] <- t(mtx)
+  terra::values(context) <- t(mtx)
   return(context)
 }
diff --git a/R/landscapeR-package.R b/R/landscapeR-package.R
@@ -21,8 +21,7 @@
 #' }
 #' @details Check out the vignette illustrating the use of landscapeR.\cr
 #' Also: \url{https://github.com/dariomasante/landscapeR}
-#' @docType package
 #' @name landscapeR-package
 #' @aliases landscapeR
-#" @author Dario Masante
+#" @author Dario Masante [aut, cre], Lora Murphy [ctb]
 NULL
diff --git a/R/makeClass.R b/R/makeClass.R
@@ -1,19 +1,19 @@
 #' Create a class of patches.
 #'
 #' @inheritParams makePatch
-#" @param context Raster object, a raster of an empty landscape or a mask, indicating where the patch cannot be generated (see \code{bgr} argument).
+#" @param context SpatRaster object, a raster of an empty landscape or a mask, indicating where the patch cannot be generated (see \code{bgr} argument).
 #' @param npatch number of patches per class
 #' @param size integer. The size of patches, as number of raster cells. A single integer can be provided, in which case all patches will have that size.
 #' @param pts integer or matrix. The seed point location around which the patches are built (random points are given by default). It can be an integer, as indexes of the cells in the raster, or a two columns matrix indicating x and y coordinates.
-#" @return A RasterLayer object, or a vector of cell numbers  if \code{rast=FALSE}.
+#" @return A SpatRaster object, or a vector of cell numbers  if \code{rast=FALSE}.
 #' @details The patches created can be contiguous, therefore resembling a single patch with size
 #' equal to the sum of contiguous cells. The patches are created starting from the seed points (if provided) and iteratively sampling randomly neighbouring cells at the edge of the patch, according to von Neumann neighbourhood (four cells, aka Rook case).
 #' There is a tolerance of +/- 3 cells from the patch size declared in \code{size} argument.
 #' @examples
-#" library(raster)
-#"
-#" m = matrix(0, 33, 33)
-#" r = raster(m, xmn=0, xmx=10, ymn=0, ymx=10)
+#" library(terra)
+#" mtx = matrix(0, 33, 33)
+#" r = rast(mtx)
+#" ext(r) = c(0, 10, 0, 10)
 #' num = 5
 #' size = 15
 #' rr = makeClass(r, num, size)
@@ -27,19 +27,27 @@
 #' @export
 makeClass <- function(context, npatch, size, pts = NULL, bgr=0, edge=FALSE, rast=TRUE, val=1){
   if(length(npatch) != 1){ stop('A single integer value must be provided to argument "npatch"') }
-  if(length(val) > 1){ stop("A single value only is admitted for "val" argument.") }
-  if(val %in% bgr){ warning("Value to attribute to patches same as background cells value (arg. "val" equals "bgr").") }
+  if(length(val) > 1 && length(val) != npatch){ stop("The "val" argument must either be of length 1 or npatch.") }
+  if(any(val %in% bgr)){ warning("Value to attribute to patches same as background cells value (arg. "val" equals "bgr").") }
   if(length(size) != npatch & length(size) > 1){ stop('Number of patches not matching the length of size vector') }
   if(any(is.na(size) | size <=0)){ stop('Invalid "size" argument provided.') }
-  if(npatch <= 0 | npatch > length(context) | is.na(npatch)) { stop("Invalid number of patches required (e.g. more than available landscape cells). Check argument "npatch".") }
+  if(npatch <= 0 | npatch > terra::ncell(context) | is.na(npatch)) { stop("Invalid number of patches required (e.g. more than available landscape cells). Check argument "npatch".") }
   if(rast==TRUE & edge==TRUE){
     edge=FALSE
     warning('Edge output reset to FALSE. edge=TRUE only when raster output is not required (i.e. rast=FALSE)')
   }
-  mtx <- t(raster::as.matrix(context))
+  #----- LEM: the as.numeric is required for type matching in Rcpp -----------#
+  mtx <- terra::as.matrix(context, wide=T)
+  mtx <- t(matrix(as.numeric(mtx), ncol=ncol(mtx), nrow=nrow(mtx)))
   if(length(size)==1){
     size <- rep(size, npatch)
   }
+
+  #----- LEM: If val is single, expand to npatch -----------------------------#
+  if (length(val) == 1) {
+    val = rep(val, npatch)
+  }
+
   bgrCells <- which(is.element(mtx, bgr))
   if(length(bgrCells) == 0){
     stop('No background cells available with value ', bgr, '. Try checking argument "bgr".')
@@ -68,18 +76,20 @@ makeClass <- function(context, npatch, size, pts = NULL, bgr=0, edge=FALSE, rast
   }
   lst <- list()
   for(np in 1:npatch){
-    l <- makePatch(context=mtx, spt=pts[np], size=size[np], bgr=bgr, edge=edge, val=val, rast = FALSE)
+    l <- makePatch(context=mtx, spt=pts[np], size=size[np], bgr=bgr, edge=edge, val=val[np], rast = FALSE)
     if(edge==TRUE){
       eg <- l[[2]]
       l <- l[[1]]
       lst[[np]] <- list(l, eg)
     } else {
       lst[[np]] <- l
     }
-    .assignValues(val, l, mtx) #mtx[l] <- val
+    .assignValues(val[np], l, mtx) #mtx[l] <- val
   }
   if(rast == TRUE) {
-    context[unlist(lst)] <- val
+    for(np in 1:npatch){
+      context[unlist(lst[[np]])] <- val[np]
+    }
     return(context)
   } else {
     return(lst)

diff --git a/R/makeLine.R b/R/makeLine.R
@@ -9,14 +9,15 @@
 #' @param direction numeric. The direction towards which the patch will point and grow, expressed in degrees between 0 and 360.
 #' @param convol numeric. Level of convolution to be assigned to the patch (default is \code{convol=0.5}). A value
 #' between 0 and 1, where 0 is no convolution at all (basically a straight line) and 1 is maximum convolution (i.e. tends to form a circular patch).
-#" @return A vector of raster cell numbers, or a RasterLayer object if \code{rast=TRUE}. If \code{edge=TRUE} a
+#" @return A vector of raster cell numbers, or a SpatRaster object if \code{rast=TRUE}. If \code{edge=TRUE} a
 #' list of two vectors is returned: one for the inner raster cells and the second for cells at the edge of the patch.
 #' @details For any values of \code{convol} > 0.8, no big differences are observed noted. Also direction is progressively lost
 #' as convolution increases.
 #' @examples
-#" library(raster)
+#" library(terra)
 #' r <- matrix(0,33,33)
-#' r <- raster(r, xmn=0, xmx=10, ymn=0, ymx=10)
+#' r <- rast(r)
+#' ext(r) = c(0, 10, 0, 10)
 #' plot(makeLine(r, size=50, spt = 545, direction=45, convol=0.05, rast=TRUE))
 #'
 #' @export
@@ -28,7 +29,9 @@ makeLine <- function(context, size, direction=NULL, convol=0.5, spt=NULL, bgr=0,
       }
       spt <- .toCellIndex(context, spt)
     }
-    mtx <- t(raster::as.matrix(context))
+    #----- LEM: the as.numeric is required for type matching in Rcpp ---------#
+    mtx <- terra::as.matrix(context, wide=T)
+    mtx <- t(matrix(as.numeric(mtx), ncol=ncol(mtx), nrow=nrow(mtx)))
   } else {
     mtx <- context
   }
@@ -79,7 +82,7 @@ makeLine <- function(context, size, direction=NULL, convol=0.5, spt=NULL, bgr=0,
     }
   }
   if(rast == TRUE) {
-    context[] <- t(mtx)
+    terra::values(context) <- t(mtx)
     return(context)
   } else if (edge == TRUE) {
     edgVal <- ifelse(val+1 == bgr, val+2, val+1)
@@ -101,7 +104,9 @@ makeLine <- function(context, size, direction=NULL, convol=0.5, spt=NULL, bgr=0,
       }
       spt <- .toCellIndex(context, spt)
     }
-    mtx <- t(raster::as.matrix(context))
+    #----- LEM: the as.numeric is required for type matching in Rcpp ---------#
+    mtx <- terra::as.matrix(context, wide=T)
+    mtx <- t(matrix(as.numeric(mtx), ncol=ncol(mtx), nrow=nrow(mtx)))
   } else {
     mtx <- context
   }
@@ -149,7 +154,7 @@ makeLine <- function(context, size, direction=NULL, convol=0.5, spt=NULL, bgr=0,
     }
   }
   if(rast == TRUE) {
-    context[] <- t(mtx)
+    terra::values(context) <- t(mtx)
     return(context)
   } else if (edge == TRUE) {
     if(val+1 == bgr){